The Son
by Jezaray
Summary: Jor-El lives! Crossover with Xmen. Clark gets caught between the will of his father and the power struggle between Jor-El and the earth mutants
1. Chapter One

Disclaimer: Neither Smallville nor Xmen belongs to me; I am not receiving any money. (Literally!)

Summary: AU. Jor-El lives! Crossover with X-men. Clark gets caught between the will of his father and the power struggle between Jor-El and the earth mutants.

Author Notes: This story is focused on the Smallville universe, disregarding the future for now. AU but doesn't necessarily mean Superman isn't going to come to be, I'm just not including it in this storyline. Also, the mutants from the X-men universe aren't well known, with the exception of the majority of the government and those who have come in contact with the X gene. 

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Jor-El carefully looked over the documents in his hands, scanning the numbers and statistics dotted over them. _This is good. Good for me, anyways. He could tell that some others were not going to be very happy on this fine fall morning. Outside, the rain had stopped, leaving a partly clear sky and a distinct smell in the air. The building was built of stone and looked run down and eroded by the elements that rolled over the mountain side. Tall pines surrounded his ledge in the forest, leaving all but a patch of sky above cast in shadow, and the grassy slope that ended abruptly down at the tree line was gray. _

Jor-El sat thoughtfully, contemplating sleep. He was a bit tired, yes, but felt empowered. His keen sense of hearing caught scraping of bare feet on the stone floor several stories down. The sound became steadily louder. 

The door creaked as weight was placed near its base. 

"Come in." Jor-El allowed, before the man outside even had a chance to knock. His heavy frame leaned through the door, disguised by strange, thick clothing. The man's arms hung loosely at his sides, knotted with muscle. 

"Someone's here." He grumbled, waiting for a response.

Jor-El nodded slowly, deliberating. "I suspected that might be the case. Send them in." The door swung back, parted slightly. Some time later, a slim hand slipped into the crack, widening it, and someone entered the room, slow and deliberate.

Surprisingly enough, it was a woman, of short stature. Dressed cleanly in a pleated skirt and jacket, she held a leather briefcase at her side. He raised an eyebrow at her over his fingertips, long fingers arched and touching lightly in front of his face. He waited patiently and calmly, and she cleared her throat, taking an available seat. Finding it uncomfortable, she shifted, eyes never leaving his composed face and inquisitively arched eyebrows. 

"So." He said, amused. "You found me."

"If you don't mind me saying so," the woman said, collecting herself. "You left a bit of a trail behind you … by all appearances, you wanted to be found. Here I am." She leaned back.

He nodded, still amused. "Well, it would seem so, wouldn't it? Do you like my humble abode? It's a bit cold in the winter, but I have to admit it's never disturbed me. It bothers Thomas. Perhaps I will have some sort of heating installed."

"Was there anything you wished to say to the person I represent?"

He shrugged. "That depends, of course, on what you have to say to me?"

She calmly opened her briefcase, pulling out a stack of papers and straightening it before herself. "You've become quite well known. At least… to those interested in things that aren't well known. I don't think you will be explaining yourself or your actions any time soon?"

Jor-El shook his head. "My question is, if you've been aware of me for very long, why wasn't I approached before now?"

Her face remained expressionless. "The one I represent would be interested in meeting with you, perhaps coming to an understanding."

"Of course he wants to meet me."

"The two of you seem to have common interests."

"It may be so." Jor-El smiled to himself. "Or, per say, his interests align with mine… in that case, I'm sure we can work something out."

She wasn't surprised. "Magneto has no desire to work for you, sir."

He nodded. "For now."

She drew her hands to herself, unsure. Jor-El watched with a keen eye. "You have an interesting bone structure, my dear."

She blinked. "You're a mutant? I wouldn't be surprised."

"Please reveal yourself."

Her features shifted, brown hair shrinking up into her scalp, and skin darkening to blue. He laughed, and she looked offended.

"Some other time." He said curtly.

Confused and silent she took her briefcase and left. Sliding the wooden panel that was the wall, Jor-El left his documents to the side and turned his attention to his many blue computer screens. An attack was gathering; he was sure of it. 

He gazed out the window to the gray foliage outside, where the sun shone bleakly through the tips of the trees. _Maybe it was time._

It was several hours before anybody realized he was gone. 


	2. Chapter Two

Author Notes:  Fun. I've been dreaming of this storyline for several nights in a row (I do this often) so I figured it was time to write it down, I hope you enjoy it, please review! Also, am I spelling Jor-El right? Is it with a hyphen, or what? 

The time line for this story is thus- Some time after X2 and right before the end of Smallville season two, so Clark hasn't blown up the ship or encountered his father.

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Jor-El stopped his flight, landing noiselessly. The person in the room underneath seemed to sense his presence, and moments later a door creaked open and a dark head appeared below. 

"Is there anyone out here? Mom, Dad?"

Jor-El smiled ironically, but stayed silent. The young man below stepped out, seemingly unafraid of what might lurk in the pitch black of the cornfield beyond.  Due to the clouded sky, the night was moonless and profoundly dismal looking. 

_Surprised Jor-El? Maybe the time came years ago, you've let your son grow up._

_That was the point! _He thought irritably. Perhaps to prove something to himself, he cleared his throat loudly, slipping down to the earth by the door. The boy's head whipped around, startled. Jor-El let his eyes smile, his face impassive.

-**Hello.-**

The boy seemed to take this well. He didn't step backward, instead he took a step forward, which was unexpected, if not pleasantly surprising. Jor-El was good at reading human emotions, a given after eleven years of living among them. The mutants seemed to be greatly similar to the humans, anyway. The way people acted really said a lot about them, it was a genuinely fascinating, a hobby of his. 

He turned his attention back to what was in front of him. The boy didn't seem to be having much of a reaction at all; the his father's voice seemed to have put him in a bit of a trance. Jor-El turned, glance flickering over the farm, and headed for the storm cellar. He knew that he would be followed

Down a short stretch of steps, metal gleamed dully. He ran his hands over its smooth surface, closing his eyes. 

**–This brings back memories… you too?-**

"Not really." He shrugged a bit. "You are... who are you?"

**-That's a bit obvious, my son.-**

The boy closed his eyes. "You were dead."

**-One could call the state I was in so. But no, not in the way you mean it.-**

He seemed at a loss at what to say. He turned his face away, to some forgotten corner of the room. Jor-El watched him with a certain pride- there was obvious strength and intelligence, and similarities between the two of them that were plain to the eyes. Perhaps that's why the boy had hesitated.

**-You want to know what happened, I'm guessing. And what I'm doing here now?-**

"Yes."

**-Perhaps we shall go talk. The sounds of the plants growing is soothing, and quite pretty. You hear it?-**

The boy shook his head, eyes unfocused, a bit lost.

____________________________________________________________________

Clark felt like he was about to start shaking any second. He felt like he couldn't look up, but he did, and the man was still there. _The one thing I never thought would happen. _ His thoughts strayed to his parents asleep in the house. 

He didn't know what to think, there were so many thoughts in his head it was overpowering. Everything felt ripped out from under him… what the hell was going to happen now? Would his father… go away? Would he try to take Clark with him? What had happened, if his father was alive, that he had come to the Kents, and the meteor shower? What about the message Dr. Swann had, was it a fake? A lie? How much had been a lie? Why was he even here? What had his father come from?

… was his _mother still alive?_

Clark felt eyes on him and look up. His … father's eyes were darker than his own, and piercing. The planes of his face were similar, and he was even taller than Clark himself. Hi shoulders were wide and the figure imposed on the quiet serenity of the corn field, except for the moments where he blended in naturally with the shadows. He was wearing a long black cloak that seemed to be impervious to the wind, strong gusts barely rippling along the edges. 

Clark's muscles tensed up as they entered the tall, obscuring field. His father's eyes watched him closely, a strange look in them, and Clark felt uneasy. Seeing Clark gazing back, his face softened. Their pace slowed, and the tall man's face lifted to the sky. His shoulders seem to brush the cornstalks on both sides. Before this imposing figure, Clark felt a twinge of fear. There was no doubt this powerful man could obliterate him if he wanted. _What does he want?_

**-So.-**

The voice seemed to resonate from somewhere within his own mind, but it was foreign and intrusive. Not probing, but it cut through his thoughts to the front of his mind. Clark breathed in, shutting his eyes momentarily.

**-You are my son, and I named you Kal-El.-**

"I've read your message." Clark blurted out. The eyes watching him seemed to have an unearthly glow as the moon peered between the clouds. "Your infant son… your last hope… what was that all about?"

The man seemed to sigh, but it was nothing audible. They plunged back into darkness.

**-The message was brought out of desperation. I was trying to spare you from further harm.-**

"Further harm?"

**-The message, as well as the one I left for you, here.- **He made no movement, but he obviously meant the ship they had left behind. **–Were to remind you where you were from, and who you belonged to.-**

It didn't seem odd at all, to be standing there in the dark. There was purpose to the silence. 

**-Our planet fell apart. It wasn't a sudden thing. It started with the earth shaking and groaning, buildings collapsing. Then cracks appeared… The original reason is lost. Somebody must have known, but they didn't tell. Maybe one day we will know.-**

They way he said this gave Clark the impression that was not going to continue, but when he did, it surprised him.

**-I came home one day to find everything gone. There was a huge hole in the ground where it had caved in, and the place I called my home and fallen apart and lay in ruins. You survived.- **He breathed deep, in grief. **–Your mother did not.-**

Clark felt a twinge of pain for the person he had never knew. 

**-The end was coming, and everyone knew it. I sent you off. I knew it would be better that way. Surprisingly enough, some of us survived. We moved on, and some time later we had spread out through our galaxy. There was only one place I could think of going. I came here, to see what had become of my only child…-**

"They call me Clark." The man blinked at this, absorbing it. 

**-I found you safe and happy. I was dead inside, everything that was mine had been ripped away, and I found myself lost… I couldn't bare to be reminded. Not able to tear myself away I found a place on Earth. I left you here.- **

Clark bent his head down. 

**-I have healed. Perhaps. Or maybe it is just time.-**

"The message. You said… you said to rule them with strength." His hands curled involuntarily.

Jor-El deliberated this. **–They are a flawed race indeed. -**

Clark turned back to the farmhouse, where a light on the porch suddenly flipped on.

"CLARK?" Jonathan's silhouette appeared. An iron hand came down on Clark's shoulder, and he started. ****

**-Be silent.-**

Clark was unsure of what to do. 

**_–Why?-_** he asked tentatively.

**-We must move on now.-**

**_-We're… leaving?-_**

****

**-For now. You object?-**

Clark was torn. He couldn't leave, not now, when he life was going right, everybody would worry about him. The concept of simply leaving without saying goodbye was inconceivable.

**-At least for now… you are my son, and it was I who named you. I sense your reluctance, yet as your father I expect a certain obedience.-**

A chill ran through Clark's blood. 

**-You will do as I say. This is disagreeable?-**

Clark shook his head mutely. Fingers hooked around the neck of his shirt, taking firm hold, and suddenly his feet left the ground as he shot straight up and the farm disappeared in a gray blur. 

____________________________________________________________________

Jonathan looked out from his house. Something in the corn field rustled loudly and suddenly. 

He looked uncertainly towards the barn. "Clark?"

_He probably fell asleep in the loft again… I'll get him tomarrow._


	3. Chapter Three

Author Notes: Thanks for reviewing.

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Clark slept with his arms stretched over his head, elbows bent and fingers curled loosely. Slowly he woke, blinking and stretching his arms, perplexed by the feel of soft linen sheets and an unfamiliar mattress. He opened his eyes to a fairly large white room with wooden furnishings, and a large stone-laid window that looked out into a sea of green trees.  He leaned against the windowsill, peering out curiously.

_Whoa. Where am I?_

He sighed as he went over the events of his departure the night before. His parents were sure to be worried about him. What was he doing here? _My father asked me to come… my father! My real father. Someone like me. How can I give up this chance to find out where he lives, to get to know him?_

_We FLEW. We could be in Europe or something… I wouldn't know where to go even if I tried to leave._

_Maybe I'll learn to fly, too. _Clark thought of his fear of heights and winced, pushing them aside. 

A murmur of voices floated to his keen ears and he opened the wood door, looking out into a stone hallway. He prowled down the long corridor, finding a set of steps at the end, down to where a heavy door was shut securely, distinct sound of conversation managing to escape through it.  The knob slid open smoothly and Clark stepped into the room. 

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"The building I have situated in the heart of New York has been pinpointed for sure. The only question is how soon they're going to take action-"

Malady heard the door click and her eyes flicked up and away from her fingers, playing with the bangles on her wrist. Surprised, she blinked. _Who the hell? _A tall guy with dark hair stood in the doorway. His hair was tousled, and he wore a loose white shirt and pale jeans. He looked vaguely sleepy, and he looked heavy-lidded over them and ended upon Jor-El. 

She leaned forward to get a better look at Jor-El around Meatface's bulk. Meatface leaned forward as well, and she glared, irritated. The Hunter was a huge man with bizarrely disproportionate muscle and beady eyes that always seemed to be peering at her from his heavy face. _Meatface__ couldn't be any uglier if he tried._

Finally she managed to lock her eyes upon Jor-El. He didn't look surprised to see the sudden visitor at all. Jor-El was strikingly handsome as always, and the usual calm mysterious expression was set into his eyes. Malady bit her lip slightly. Attractive, unattainable, and boss.

Thomas practically dropped the stack of papers he was holding. "Who are you?!" he demanded.

"This," Jor-El interrupted smoothly, "Is my son, Kal-El."

Everybody stopped. _Son.__ Jor-El has a son. Where and when did that come from?!_

_Really, one of them is enough. _Malady _did_ enjoy Jor-El's company, however, and if his… son… was anything like him, things were sure to be interesting. 

"Kal these are a few of my employees… Thomas, The Hunter, Malady, and Ras. I'll be out to speak with you shortly, we have some business to wrap up."

The son – the similarities between them were uncanny, really- nodded and exited quietly. 

____________________________________________________________________

Wolverine glared out the window of the Institute, finding anger for the peaceful front lawn and rows of flowers. _This Jor-El character is really starting to piss me off. _"We know where he is… why don't we just attack now?"

"Because 'Jor' is so rich, that the notion that he is staying in that particular house, is highly unlikely." Cyclops criticized, ignoring Wolferine's irritation. "Furthermore, we know nothing about him or his resources. Just look at this! He's kidnapped 25 mutants in the last year… what could he possibly be up to?"

"There's no clear motive as far as I can see." Ororo said. "He has taken over several major industries, as well, and has orchestrated the downfall of many large companies. All these seemingly random companies, small businesses, and buildings seem to belong to him. Several even go under the name of LuthorCorp, yet he controls them."

A noise from the doorway made them turn around. The Professor pushed his wheelchair into the room and joined them. "I have found the identities of the four mutants that he seemed to have taken as his main underlings. We've seen them together with him many times. The woman is Elizabeth D'Anthes, she has a way with computers. She can get into them similar to a computer virus, and go through files and destroy them. She's known as the mutant "Malady". Then there's Thomas Clifes… apparently he has no physical manifestation of the mutant gene, yet he has an extraordinary genius and has a capacity to store almost indefinite amounts of information in his brain. The large one is known as Jor-El's second in command, and his identity is lost to me… he's known only as 'The Hunter'. The last is Julian Well. There is no record of him using a mutation lately, though we'll assume there's one there."

Ororo's shoulders slumped. "What's our next move, Professor?"

"We should see what we can discover by looking into his 'factories', and what he keeps there. Maybe we kind find out what he's about."

"He kidnaps mutants, steals money and technology, has his own underground empire, and seems to be willing to do anything to gain more power. That's enough for me." Wolverine growled.

"We must proceed with caution. Jor-El himself is the greatest mystery. I'm positive he is a mutant, thought I haven't been able to find him or the others with Cerebro. What powers he has is beyond me, they must be great. The ones we intercepted were unable to give us any information, they were all terrified of him."

"So we've got a superpsycho manic-powerful mutant on our hands… but we knew that already, right?"

____________________________________________________________________

"So they're different from the meteor mutants..." Clark nodded at his father.

"Yes. They're useful than the average human, I prefer their employment to that of the others. They have distinct uses to me."

"The four in there are mutants, then."

"Certainly." Jor-El stood, motioning with a tilt of his head that Clark was to follow him.  The central staircase that seemed to conveniently lead everywhere twisted down into a large windowless room where a fire blazed under a large mantelpiece. The dark shadows of the room flickered forward onto the faces of the five or six people who sat around the room. In a large armchair, an old man with bits of blond in the white hair, showing what must have once been. He gazed at them with clear grey eyes, and seemed to twitch. A woman with short dark hair looked up surprised as they walked in, quickly turning back to a row of file cabinets. She seemed to be whispering furiously to herself. 

**-Do you like it here?- **The language he used was the same one as that of the caves, Clark recognized it, even spoken out loud. Or not out loud, whatever.

**_-It's nice. Very quiet.-_**

******-I prefer it so.-**

**_-What's wrong with her?-_**Clark inquired gazing curiously at the short woman in the corner.

**-She's sending instructions to my other employees. It's safer than phones or any other technology, virtually nothing can intercept her broadcast.-__**

Clark leaned against the wall by the fire looking at his father's face in the dramatic lighting. _Should I say something? I could ask him how long I'm staying here… or maybe I could call my parents. The occupants in the room were peering at them curiously. _They're probably as confused as I am.__

Jor-El switched to speaking vocally, still pointedly continuing in Kryptonian. "I have a favor to ask of you, Kal."

Clark blinked, surprised. "A favor?"

"I would do it myself, but my presence would be noticed much sooner. And I don't think any of these people could pull it off. You're my son- I have faith in you."

Clark felt apprehensive. "What exactly do you want me to do?"

"Pick up something I need."

Clark was still uneasy. "… steal it?"

"You could put it that way."

Clark looked at him silently, not sure what to say.

"I wouldn't ask if it wasn't that important. It will be easy- I'll just fly you halfway there, and then you can run the rest. Just walk into the building. It's unguarded, but has difficult security systems."

_My parents wouldn't like this._

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Clark's feet set on the ground as Jor let go of his shoulder. He was wearing all black, a long sleeved dark shirt and black jeans, boots, and even a dark mask that covered his face and hair. He peered once more at the map in his hand before handing it back.

**_-Got it.-_**

**-I'll be here when you get back.-**

**_-No problem.-_**

Clark zipped off at superspeed, confident in his direction. Within seconds he was passing through an urban community, taking the streets, dodging cars effortlessly and going deep into the city. Moving to the roofs, he found his bearings by orienting himself to a large cone-like roof. Turning left he easily jumped the buildings for several blocks and came to a stop. Between two tall, important looking buildings was a squared off, squat one. It had a large fence and the few windows visible were small and currently shuttered closed, hiding a variety for possible things- bars, wire, maybe metal sheets. 

Several moments later he walked down casually, opening the front door. Quietly the lock cracked. He walked in, taking a nearby elevator. A scientist in a lab coat saw him coming and slipped around him, running down the hall and disappearing. 

Clark leaned casually against the inside of the elevator as the floors dinged away. The rooms had all been cleared and passing through the floor not even attempting to open the doors, sometimes managing to take part of the door frame with him as well as the door. Coming to his destination, he shook himself, sending wood splinters against the white walls. There was a small room. The vault.

The far wall was covered with metal compartments, but the large one in the middle was the one that held his attention. Crunching the front together like a sheet of paper, he reached in and pulled a small electronic chip out in a clear plastic container. He held it up, peering inside.

_This isn't right. These people can't even defend themselves… _

Face contorting in anger, Clark punched the wall, watching the compartments collapse together and flatten on the floor. The sound of twisting metal echoed through the building, and next turned to the chip, about the crush it between his hands. Thinking of his father, he hesitated.

_I don't even know what this is. _

Shoulder's slumped, Clark resignedly found a nearby window, and battered through it, disappearing onto the roofs.

____________________________________________________________________

An alarm went off at the institute. The Xmen gathered around a monitor as information scrolled down it.

"Should we go?" Cyclops asked. 

"It's too late now. We should still check it out and see if we find anything." Storm said. 

She looked closer. "What the hell is that?"


End file.
